Tuesday, September 15, 2009

Nonscientists Naive about Science

I like listening to journalists talk about science, as such fields have parochial tests and models that can take years of devoted study to fully appreciate. Some of these insiders, like Steven Pinker, are good at communicating to a general audience, but most of the translation to outsiders comes from non-scientists simply because there are more of them, and some write very well.

Yet, I find many times, when these journalists digress from a specific subject, to science in general they are extremely naive or duplicitous. If you go to The Skeptic's Guide to the Universe, you invariably hear a bunch of caricatures of those who disagree with conventional wisdom on science—most of which truly are quacks, but not always—and they pedantically emphasize how these alternative views are 'not science': they have beliefs that do not have peer-reviewed tests supporting a falsifiable hypothesis. Or listen to Chris Mooney, a journalists who thinks the masses are insufficiently scientific, and argues that Republicans hate or are ignorant of science. He argues we should have more 'pro science' candidates, reflecting the 19th century progressive notion that with education, most disagreements and bad policy disappears. Most importantly, if the masses knew more, he surely thinks then popular opinion would converge to his. This from a journalist, a clan whose scientific proficiency is similar to the athleticism of mathematicians.

When journalists talk about science in general this is usually a pretext for saying those who disagree with their favorite idea are wrong, because they are unscientific. Who can be against science? There isn't a formal anti-science movement because it's indefensible in principle. They then caricature their opponents, taking the most inarticulate advocates from the other side, and skewering their illogic. They then sit back and take take inordinate pride in their scientific pretensions, as if their selective discussion was objective. The fact is, most 'big' scientific issues do not conform to the scientific method, where one puts out testable hypotheses, rejecting ones that are falsified.

Take finance, where the main potentially falsifiable theory is that there is a Stochastic Discount Factor 'like' the S&P500 index that one uses to generate 'risk', and thus the expected return, on every asset. This is a prerequisite for any rational portfolio allocation, because you need the mean for a 'mean-variance optimization algorithm' for determining one's portfolio. What is this Stochastic Discount Factor? Well, not the S&P500, though that's what is still taught in Business School via the CAPM, because we are pretty sure these betas are not correlated with returns cross sectionally anywhere. In Treasuries, it's a subset of forward rates. In equities, its a size, value, and market factor (the Fama-French factors), or it could be consumption-to-wealth ratio, where consumption is measured as nondurable consumption, and wealth comes from the Survey of Households. Or it could be year-over-year consumption growth. Bill Sharpe, who won the Nobel prize for his one factor model, also has a model with 12 factors. If it squiggles over time, it's a viable risk factor proxy. So, no one knows how to measure true risk, but presumably markets price it by aggregating everyone's preferences for this unidentified factor(s). Yet, as Andrew Lo states, "Finance is the only part of economics that works." Yikes!

To see how incredibly bizarre this situation is, consider the classic demonstration of group intelligence is the jelly-beans-in-the-jar experiment, in which the group's estimate is usually far superior to the vast majority of the individual guesses. When finance professor Jack Treynor ran the experiment in his class with a jar that held 850 beans, the group estimate was 871. Only one of the fifty-six people in the class made a better guess. So that's how risk and return work, the wisdom of crowds distills a precise truth out of our fuzzy uncertainty. Except here's the problem: no one know what risk is. It like presenting people with a jar of jelly beans, a jar of rice, a jar of rocks, and a jar of bb's, and asking them 'How many are in THE jar'? The question does not make sense; there can be no aggregation. So with respect to risk, if no one knows what it is after 40 years of searching, why should we think people agree on it sufficiently to aggregate and distill priced risk premiums. Is it any wonder we can't measure them?

Yet, if you ask financial economists how scientific their field is, you can be sure the answer will be some variation on very. For example, derivatives pioneer Mark Rubinstein paid homage to Modern Portfolio Theory creator Harry Markowitz in 2002, and noted that:

Near the end of his reign in 14 AD, the Roman emperor Augustus could boast that he had found Rome a city of brick and left it a city of marble. Markowitz can boast that he found the field of finance awash in the imprecision of English and left it with the scientific precision and insight made possible only by mathematics.

This gives the impression finance is working on the third digit of fundamental constants in finance, as opposed to finding the right sign.

But, finance should be congratulated because its errors are more conspicuous than other fields, which have similar problems. Take String Theory. Invariably any researcher is working on one aspect of the theory, and cannot comment on the theory as a whole. Alas, the main problem is they have 10^500 potential solutions, and prominent theorists saying that these actually all exist now. One of them matches our universe, but with quintgoogle universes this is unsurprising. Throw in the anthropic principle, which states we necessarily live in a universe hospitable to human life, and there we are, numbers match to a T. It does not predict, it explains, but in a meager way because it merely tries to match parameters generated from a small set of separate models using a much more complex but unified model. Complex mathematics necessarily has more degrees of freedom, so this is all pretty unsurprising, and without some novel testable hypothesis, rather pointless.

Or take astrophysics. Their theories of the early universe also tell us which atoms should have been forged in the first 5 minutes after the big bang, and the existing amounts of hydrogen and helium match theory so well that cosmologists claim this is the best evidence we have for the big bang. Yet what about the next element, lithium? There, they are off by a factor of three. They don't like to talk about that. Or background of the universe, which seems perfectly flat...except for this mystery pattern in the middle called the 'axis of evil' that does not make any sense.

But the best example of science putting lipstick on a pig is dark matter. Vera Rubin, together with Kent Ford, announced at a 1975 meeting of the American Astronomical Society the astonishing discovery that most stars in spiral galaxies orbit at roughly the same speed, which implied that their mass densities were uniform well beyond the locations with most of the stars (the galactic bulge). This result suggests that either Newtonian gravity does not apply universally (can't be) or that most of the mass of galaxies was contained in the relatively dark galactic halo. Met with skepticism, it is now conventional wisdom. But what is dark matter? The stuff needed to make Newtonian physics match galaxial reality. It's like saying X=7, but when you measure X=9, you simply say there is an extra '2' of 'dark X'. They've tried to find it, building big swimming pools underground, hoping to find evidence of the leading candidate for dark matter (WIMPS), but thus far have been no more successful than SETI.

Or take our solar system, where every planet except Jupiter is assumed to have a huge, fortuitous asteroid giving it its singular properties of spin, moon, or composition. It seems like it is more common than not to fix a flawed empirical prediction with a nonfalsifiable adjustment.

Lastly, take Darwinian evolution, the idea that all life on earth descended from a common ancestor. Now, if you define evolution as the natural processes of heredity, chance, mutation, and natural selection, I believe 100% in evolution. That is, methodological naturalism excludes any other possibility. If you don't believe in the supernatural, evolution is a tautology because whatever exists descended from something else that was both lucky and successful, statistically, and also different from but related to its ancestors. The real theory in evolution, is the mechanism, which is on much shakier ground, similar to economists understanding of business cycles.

Take the 'evidence' for evolution, which has been assumed overwhelming by conventional scientific opinion for over a century, and see how tendentious it is. Darwin thought his best evidence was Haeckel's drawings that suggested ontogeny recapitulates phylogeny, that species closer to our uber-ancestors look more like early embryos, species higher in the evolutionary tree like late embryos. We know know those drawings were frauds, and this line of reasoning is a dead end. Karl Popper gave as an example of the analytical power of evolution the existence of darker moths in industrial environments, and this example was prominent in textbooks for decades. But the signature pictures of the dark moth on the pollution-darkened tree were invariably stuck there with a pin, and not relevant to speciation. Or Darwin's famous finch beaks, that were longer when there was less food--these turned out to be temporary phenomenon, and there is no trend in finch beaks that suggests this phenomenon leads to speciation.

Darwin anticipated finding all sorts of intermediate forms in evolution, but these are the exception, not the rule. Indeed, Gould's punctuated equilibrium theory was first seen as untrue, but then, a minor change in emphasis that Darwin's theory allowed all the time. There is much effort to show Darwin did not reject sudden changes, but clearly the Origin of Species emphasized the smaller steps. One can argue that 'sudden' in geological time is long in generations, but nonetheless, it's a major change in emphasis. The scientists like to whitewash these debates because they are scared to death of looking uncertain to Bible thumpers.

Or take Richard Dawkins, whose Selfish Gene argued evolution takes place almost entirely at gene level (ergo, selfish gene, not selfish organism), not the organism or the population. Over the past 15 years this view is now very much in doubt, as evolution at multiple levels appears equally important, with no special prominence to the gene level. Emphasis is everything because science is about probabilities, not possibilities, and so Dawkins was wrong, though he has never admitted to anything but being right all along.

The smoking gun for evolution from common descent is speciation, not local adaptation and differentiation of populations. There is no smoking gun. The mechanism of evolution is still a mystery, unless one is happy merely knowing that it's 'not God', which given methodological naturalism, is true by assumption. Nonetheless, none of these setbacks has affected believers in the theory of evolution, which even in its very incomplete state of explanation is considered perhaps the greatest scientific theory of all time. In sum, there is no debate about the tautologous portion of evolutionary theory, but mass mystery on the 'scientific' part, though they are loathe to admit it.

In all these cases, science mainly is about explanation, not prediction, and practitioners exhibit much more precision and confidence than is objectively warranted. Even in cases where there is prediction, like Global Warming, this is not falsifiable prediction. There are not unambiguous Global Warming forecasts with standard errors, such that in one's lifetime any Global Warming advocate could be proven wrong. If the world shows no trend in temperatures, it will simply be seen as temporary. There are no definitive tests in major scientific debates.

So, when some journalists talks about how horrible it is that politicians, or voters, do not understand science, which their rigorous falsification of hypotheses, I say, gimme a break. The biggest scientific debates are not about testing a definitive hypothesis, they are more often about coming up with more evidence for a metaview about some bigger truth, hardly much different than our quaint medieval ancestors. The big ideas are fun to think about, and I have opinions on them, but I'm not naive enough to think these debates are subject to the ideals of THE scientific method, where only objective, rational empiricism is involved. Tests that don't go our way are dismissed, tests that favor our predisposition are emphasized.

If you don't think that is true, think about how many Keynesian economists became supply siders over their career, or supply siders who became Keynesians. Think about the market efficiency debate, where irrationalists (eg, Thaler, Shliefer, Stiglitz) are against those who see the markets as rational (eg, Fama, Cochrane, and French). I would estimate less than 5% of economists change sides over their working lives. Yet, they are all scientists, use logic, examine data, publish in peer reviewed journals, understand statistics, and generally think they have good faith trying to understand the world as it is. The data seem rather unconvincing to diametric views on the big ideas within any field.

God is dead, but faith did not disappear. Rather, people always have faith in whatever they think is really important. With God out, now what is important is some big cause that, when fixed, will create a better world. As Eric Hoffer noted in The True Believer, 'all mass movements are interchangeable', meaning nationalistic, religious, social, political movements have the same true believers. Western civilization has tossed off nationalism and religion, but we are just as ideological as ever, only now we pride ourselves that our beliefs in social or ecological justice as the result of truth, divined through science. If only.

It is good to have the facts on your side because it makes it a lot easier to argue your case, but in real time any big debate necessarily will have ambiguous facts for the simple reason that if the data were definitive there would not be a debate. Further, important matters necessarily have a debate, because there if there's no debate one takes it for granted, as opposed to seeing it as something noble to fight for. In this cynical view of the world, it is best to have common sense, which Einstein said 'is nothing more than a deposit of prejudices laid down in the mind before you reach eighteen.'

Science as a practical matter is about applying logic to data piecemeal. Isaac Newton made huge contributions to optics, and created calculus so he could prove the laws of motion. He also had bat-shiat crazy ideas about alchemy and Biblically based numerology, and thought his greatest achievement was dying a virgin. And that's as good as it gets.

133 comments:

I would argue that God is alive and well in whatever each individual chooses to worship.

Some Gods are spiritual in nature, some Gods are secular in nature, depending on the preferences of the worshiper.

God exists in whatever an individual chooses to put his/her faith in.

It's pretty funny to see these Science-types putting down "religious zealots", when all the while they are slavishly and absurdly following after their God of Science, ignoring ambiguities and contradictions equal to anything in any spiritually-based religion.

None of us are the exempt from the human need to believe in some organizing principle, to have something to put our faith into, even if it means "believing in no God". (Which is not the same as not believing at all)

Thanks for writing on this topic, it is very interesting and valuable.

Anyway, we know that science does not explain the universe, but it is extraordinarily good at making things work. The fluid mechanics of an airplane are so complex that no one knows how to calculate all the eddies and so on, but fly it does. Molecular genetics works, we have plants producing human hormones. We dont know what probability is, but you are good at calculating it. Even risks are rutinely estimated, just look at insurance companies and their steady stream of dividends.

J: I didn't mean to imply science isn't productive, only the big questions are much less scientific. A well defined problem is usually not a big question, and science is good at little issues, like mean-variance optimization, or OLS.

Hello! I happen to listen to the Skeptic's Guide to the Universe. I don't think you give them enough credit for what they're actually trying to accomplish. Its undoutedly true that they will often stumble when they speak about issues outside of their area of expertise (Economics, Political Science, Meta-issues), but they are usually spot on when discussing the physical/biological sciences and run of the mill supernatural goblety-gook. I think that on balance, the average listener is likely to leave generally more informed about issues that probably matter quite a bit in their daily lives, such as avoiding the palm-reader or dealing with the conspiracy theorist talking about how the LHC is going to blow the world up.

I prefer to just tune out when they try to get any more meta-level than that. Although to their credit, they often mention when they have stepped outside their comfort zone.

Based upon your criticisms of evolution I struggle to credit the thesis of your article. Yes, the photographs of the moths were posed in order to illustrate the point, but the actual data was not faked - this is a poorly chosen example. The Haeckel example also fails for much the same reason - yes he drew the pictures to exaggerate certain similarities, but embryos of different organisms DO show similar characteristics during development. Modern evolutionary theory does not rely in any way upon Haeckels drawings. In fact Darwin did NOT think this was his best evidence for evolution, he barely mentions Haeckel at all - not surprising since the Origin of Species was published in 1866 and the drawings in 1874. The "evolution as tautology" argument has been widely viewed as incorrect by many philosophers. The species concept in most of modern biology is largely used as a taxonomic convenience, representing rather arbitrary phenotypic distinctions and thus I am not sure that there is the "speciation" problem you describe.The concepts and predictions of evolution are used daily by biologists, just as Newtonian mechanics is used by physicists and engineers. Are any of these complete explanations? No. Are they "true", yes.It seems that much of this section derives from the discredited creationist text "Icons of Evolution", by Johnathon Wells or similar. Given that this scholarship is so woeful, why should I believe any of the rest of your article? You seem to have unwittingly become one of the very caricatures that you so criticised others for "selecting" in the first paragraph of your article.

alan17: my point was not that these criticism are devastating to evolution, but rather, they highlight how crucial evidence, when shown wrong, or at least much less supportive (clearly Haekel's drawing take some rather subjective decisions about timing, which to include), they do not re-evaluate the theory, rather, they highlight new 'definitive proof'. I know many think evolution is not a tautology, and in principle it could be, but as actually applied, I don't think it anything but a tautology (ie, given the scientific constraints of methodological naturalism, the general idea must be true).

I disagree - none of the things you highlight were "crucial evidence". Indeed the really crucial evidence for evolution; a mechanism for inheritance, was admitted by Darwin to be missing at the time. However, the theory was still accepted since it explained so much.Both prior to and since the discovery of DNA, much of the mechanistic theory has been reformulated, after all population genetics was the forge of modern statistical analysis. Indeed, you hint at these changes yourself by citing the gene vs other levels of selection and punctuated equilibrium arguments. However, none of these challenged the real power of the theory, which (and I would argue of any theory) is explanatory and synthetic. Evolution explained so many things about the natural world that were previously opaque, such as common features of animals, spread of antibiotic resistance and now DNA sequence similarities and differences (this might be thought of as a prediction, Darwin postulated the properties of any mechanism of inheritance would have to have).The theory is thought to be true because it explains and groups so many observations beneath a simple umbrella (so simple that you characterise it as being obviously true). However, one might come up with alternative explanations, such as environmental effects actually "imprinting" beneficial traits upon offspring - indeed we now know that some of this "Lamarkian" mechanism exists, we call it epigenetics (I simplify of course).I think you miss the "common ancestor" part from the tautology - there is no obvious need to postulate common ancestry a priori, there might have been many independent initiations of life, at different times (but this is not what the evidence indicates). I think that we see the power and simplicity of Darwin's theory and think "it must be true", but this is largely a failure of imagination. Without the evidence, or with significant conflicting evidence (as JBS Haldane put it with "a rabbit in the pre-Cambrian") it would not be so. One can consider that there might have been other evidence discovered that would have led to different conclusions.One might as well say that Newtonian mechanics is a tautology, since it predicts the movement of balls, by observing the movement of balls - and given the constraints of methodological naturalism it must be true. Yet since Einstein showed that Newtonian mechanics was flawed in some circumstances, then should we not re-evaluate all our Newtonian engineering theories?Or am I missing something crucial?

I think for evolutionary theory to be nontautological, one has to be rather specific as to the mechanism. Darwin did not understand genetics, and had a vague idea about inheritance via mother and father, but he clearly highlighted small improvements. Indeed, in the book Einstein's Luck, the author argues if Darwin knew Mendelian genetics, it would have dissuaded Darwin, because it does not generate the massive amount of change needed for speciation.

I think farmers, and dog breeders understand microevolution, and use this very much, but they did this before Darwin too.

One could say Darwin did better than Lamark because his mechanism described natural variation one sees in children from there parents, and one can understand selection. Yet, when we this is put into simple theories, with simple random mutations, I don't think this climbs mount improbable, it gets stuck on local maxima.

We do understand and rutinely use microevolution, microphysics, microstatistics, and it works. You seem unhappy that we know little or nothing of macroevolution, macrophysics, etc. Let say those macro realities are useless for survival and we did not evolve a brain to solve those problems, and we are even unable to define the macro issues. Another possibility is that God started all and keeps it going.

The distinction between micro and macro evolution is a false one, it is basically determined by the time given for the change. If you accept that "microevolution" can happen, then the same mechanisms over longer time will yield "macroevolution".It is important to recognise that evolution/generation of variation operates via many mechanisms. Single mutations, genetic and chromosomal rearrangements, viral transposition - it is estimated that each human has over 100 "new" mutations (single base changes, compared to either parent). Selection also operates via different environmental factors, including sexual selection (one of the most potent speciation drivers, see African Lake Cichlids). I am not certain that genetics does not produce the "massive" amount of variation required for speciation. For example, some insects have genitalia that bend to the right, they can only mate with other such insects. A small change (single mutation, genetic rearrangement or whatever) can invert development of the genitals and generate an insect with left-leaning genitalia - this insect will only be able to mate with other mutants and this causes a speciation event. Indeed, slow drift in isolated populations also causes speciation and this can be observed in the wild. This also illustrates the problem of defining species, since such oddities as ring species occur. The progression is gradual around the "ring" but the two populations closest to one another are separated by a "species barrier", if one were to follow the ring around then one might group them all as a single species, yet the two ends do not interbreed.I am not certain that what Darwin understood or not is relevant, if he had gone off on the wrong track someone else would have come up with variation and selection eventually, indeed Wallace already had! I agree with your assessment of human breeding of animals, this is why Darwin termed his theory Natural selection - the insight was to extend the observations of breeders to explain the diversity of all life, and that natural forces shaped this, with human selection an additional force in certain special circumstances.You are correct that a grossly oversimplified model of evolution gets stuck at local maxima, however we know that variation generation is more complex. Also less fit members can still breed (albeit at a lower rate) so you can "drive around the mountain", given a large enough population size. Finally, how do we know that evolution is not repeatedly stuck at local maxima for many traits? Brain size could be increased in humans if the brain were extended to a long, thin organ that extended into the abdomen, but this is unlikely to happen - does this mean that brain size in humans is at a "local maximum". Evolution does not aspire to some final goal, or constant improvement - good enough is good enough (relative to other members of the population). Likewise, simple theories of economics fail to explain the observed behaviours, yet this does not mean that supply and demand principles do not operate.

"It is good to have the facts on your side because it makes it a lot easier to argue your case, but in real time any big debate necessarily will have ambiguous facts for the simple reason that if the data were definitive there would not be a debate."

Ha.

Haha.

Hahahahahahahahaha.

"If facts were definitive there would not be a debate"?

My goodness. I'm sorry, but that was just so funny.

Let's put it this way. The facts are unequivocal that the Holocaust happened, but there are still Holocaust deniers. The facts are unequivocal that the U.S. Government was not behind 9/11, but we still have the 9/11 "Truth" movement. The facts are unequivocal that water does not have memory and that diluting a substance to virtually zero does not make it stronger, but we still have homeopaths.

Where on earth have you been? You're either incredibly naive or utterly disingenuous.

orac: the crank ideas are not debates. I don't know anyone, personally, who believes in those examples you give, though I know some people believe them. I think you can distinguish between crackpot ideas, as these are held by such a small number of people with little credibility, they don't matter.

I agree that one can distinguish between crackpot ideas and legitimate scientific criticism. However, YOU apparently cannot do this, since you're parroting creationist propaganda as if it were legitimate.

The venom generated by questioning the evolutionary mechanism highlights this is now a 'taboo' subject. I'm not a professional journalist, so it does not constrain me, but clearly, no one wants to work in this field can do this and remain welcome among colleagues. I just find the mechanism as currently described insufficient, it's missing something, and advocates pretend like it works great, which I don't think is a good description of the theory. But as the theme of this post tries to argue, that's true for most 'big' issues in science.

Yes, it's missing something, but there are many of us who aren't ignoring that problem. One of which is to convince others that research into the way the experiences of life forms themselves contribute to their own evolution is not heretical.

Mr. Falkenstein, you really need to read the criticism of your comments by Dr. Novella as linked to above. I'm sorry, sir, but your ideas and opinions of evolution--expressed in an article ostensibly about naivete--are very naive. Your warnings might not be without merit, but your examples are. Moreover, if you're going to argue against the adequacy of natural selection as a mechanism of evolution, you would do well to be specific, and to explain the body of work establishing it's apparent adequacy.

Or perhaps you should just go read a few good books. Carroll's "The Making of the Fittest" and "Endless Forms Most Beautiful" come to mind, and Dawkins' "The Greatest Show on Earth" (out Tuesday in the US, now elsewhere) is being reviewed as precisely the book a well-meaning but evolutionarily-naive person such as yourself would want. A nice tour through the TalkOrigins Archives' Index to Creationist Claims (and other articles, such as the 29+ Evidences for Macroevolution) wouldn't hurt either, and has the advantages of getting right to the meat and being free on the web.

See what I mean? TalkOrigins, a great source, nevertheless posits that random mutations are "subjected to selection" but nothing definitive about the selection mechanism itslf - although it seems there is a concession there that the mechanism is within the organism and the mutation not somehow self-selecting because it discovers on its own that it fits in.

Um...no...I don't see what you mean. Let me try to break it down, and tell me if this helps:

You observe that TO says random mutations are subjected to natural selection. This is true, but I should add that recently mutated genes are not the only genes subjected to natural selection. ALL active genes are, though the strength of selection varies from gene to gene.

But then you say TO offers "nothing definitive" about the selection mechanism itself. This is where you lose me. I have some vague notion of where you may be going wrong when you comment about the mechanism being within the organism, but rather than waste time speculating on how exactly you're misunderstanding natural selection, let me restate natural selection in hopes that you'll grasp it better:

Natural selection refers to the differential, non-random reproductive success of organisms. That's pretty much it right there. Within populations of organisms that contain variations (in other words, they're not all clones), some of those variations will be better able to reproduce successfully than others. There are many reasons why. Simply, they may produce more offspring than others every time they reproduce. More complicatedly, they may resist diseases better, surviving more often than others to reproduce in the first place, or they may have FEWER offspring when they reproduce (producing offspring is a major burden on a parent, and in some circumstances, producing too many offspring can be detrimental to both the parents' and offsprings' survival.)

Assuming these variations are heritable--that they are passed from parents to offspring--then it follows as a simple, obvious conclusion that those variations contributing better to successful reproduction will tend to become dominant in the population. We know today that genes underlie these variations, and so we can usually discuss natural selection in terms of gene frequencies in a population. But regardless, the point is that when you have a diverse population of hereditary replicators in an environment, be they plants, animals, or sci-fi autonomous robots, you will almost certainly see natural selection because that diversity almost certainly includes features affecting their ability to reproduce successfully IN said environment. You don't even need mutation to see natural selection (though mutation is effectively impossible to avoid.)

Jaranath,The "see what I mean question" was directed to the blog author and not you, because clearly you have no idea of the nature of the selective mechanisms themselves or apparently even an inkling that there needs to be any specificity involved in their understanding. You blithely write things like "Assuming these variations are heritable" without any apparent concept of how that assumption should be made or the complicated mechanisms behind it. You're not a scientist, just someone who parrots what he has studiously read in books where the authors don't bother to deal with these particulars either. In the spirit of reciprocal condescension, I ask in return, "Did that help?"

Ah. Yes, now I understand. Now, I will say that my comments were NOT intended in ANY spirit of condescension whatsoever. I commented under a very honest, very open desire to help someone understand a topic I thought they were honestly seeking to understand themselves. I will continue to proceed in that fashion. Also, you are correct that I am not a practicing scientist. For what it's worth, however, I hold a graduate degree (MS) in biology and have a lifetime of keen interest in science in general, biology in particular, and misunderstanding of evolution most especially, under my belt. There are creationists who could claim bioscience Doctorates and more decades of lifelong interest than I. Now let's ignore qualifications and discuss selection.

You're proceeding under an assumption of agency. You're assuming that “selection” implies a “selector,” an active entity effecting the action of selection. An entity saying “You! Not good enough, go die! You! Good enough, go have offspring!” Humans are very sensitive to detecting agency, but this has the drawback of being very susceptible to false alarms, like a very sensitive radar detector without good filters that blares constantly on your morning commute thanks to every little radio-emitting device along your route.

We don't even always think of the agent as being a conscious entity; we can often see it as some sort of simple—but discrete—discriminating mechanism, such as a scale. But an aspect of natural selection is that it isn't any such agent. If it were, it would be more like artificial selection—indeed, this is why sexual selection is seen as different from, or a special case of, natural selection, because mates are making choices. Natural selection is more a simple emergent property of the ecosystem. If you have replicators playing in an environment, this will naturally happen.

Think of it this way: If you have bears in a cold environment, and there is variation in the thickness of their fur, and if the thicker fur keeps them advantageously warmer, then they of course will tend to do better. Their thinner-fur siblings will obviously have a harder time “making it” and caring for their young even if they do survive. At what point in this system did an agent say: “You! Thin-fur-bear! Tougher times for you, you'll only be able to keep one cub alive this season!” At no point. It's a simple consequence of being a thin-fur bear in a cold environment.

You're now discussing adaptive selection, an entirely different mechanism than the one posited by natural selection of randomly mutated genes. Or I should say the selective step left out when the explanation is merely that "they are subject to selection." You may need to read up on adaptive mutation, where actual biologists are studying this aspect of selection and where other and more traditional biologists are resistant to what it appears they have discovered.

Can you perhaps admit or at least pretend you've never heard of the subject? That would reflect better on you than an admission you've heard about it and dismissed it out of hand.

Mmm. Okay, I think I see where you're going, though it might help if you clearly define and contrast natural and adaptive selection. But back up a bit, I think there's some confusion of terms here. When you first spoke about TO, you spoke about their comments of random mutations being subjected to selection. You criticized them for lacking a definition of the mechanism of selection. I tried to explain the mechanism, since TO would be talking about natural selection.

It seems now that your point was that TO didn't talk about another hypothesized version of selection, which you're calling "adaptive selection." I'll get to that in a minute, but first: You understand that I was NOT talking about adaptive selection, correct? At least, not from my perspective, and I imagine from TO's as well (dunno which specific section you were referring to, but I really doubt they meant something else). I firmly place the scenarios I offered under "natural selection." I do not see them as some significantly different form of selection. Natural selection of genes that either recently or a long time ago arose via random mutation is perfectly capable of resulting in adaptations to an environment, which was what I was trying to describe.

Now, I THINK I know what you mean by adaptive selection, but I'm not sure. Are you talking about the hypotheses based on the idea that some mutations are not random? Say, research suggesting some bacteria artificially accelerate mutation rates in some of their genes under certain pressures? If so, yes, I'm familiar with it, and I know a little about some of the research behind it. I do reject it. Not out of hand, but scientifically: Tentatively, based on the weakness and scarcity of the existing evidence that I'm aware of, to the best of my limited knowledge. Indeed, whether that's your topic or not, I'd be interested in seeing links to what supporting evidence you consider best. To be pedantic, I should point out that wouldn't be "adaptive selection" but rather "natural selection acting on nonrandom (adaptive?) mutations," but again, I may not understand your topic, so a clear definition would be helpful.

I hope that reflects better on me than your implication reflects on you. In other words, I'm trying here, mmkay?

YOU were talking about adaptive selection, not me. Which is why I referenced adaptive mutation - also and perhaps better described as directed mutation. Your response would indicate an unfamiliarity with either term. Go google them. I don't furnish links to those who use mmkay at the end of a sentence.

1. I did google adaptive selection when you first mentioned it. Didn't find much useful in identifying it in a quick scan, still not finding anything relating it to biology.

2. Yes, I do know about directed mutation. That's what I was guessing at.

3. You gave me some attitude, but apparently in retaliation to perceived condescension from me, so I tried to explain that I offered none. You kept it up, so I again implied that, though getting annoyed, I was still being straight with you. I don't know what your problem is, but I don't need or want to be on the receiving end of it. Sorry to have wasted your time.

"The venom generated by questioning the evolutionary mechanism highlights this is now a 'taboo' subject"

Eric, this comment basically amounts to the assertion "A HA! Where there is smoke, there is fire!".

To be sure, where there is smoke there is often fire...but just as often there is another source...and often fire produces no smoke.

The problem is you seem to be arguing that scientists (and/or science journalists) are close-minded and stubborn when faced with criticism of their sacred cows. This of course often true, but is true of people in general.

You seem to say "Look! I provide reasonable arguments and/or objections and pose serious questions about a theory, and are greeted with such venom! A HA! See this people can't stand up to a little poking and prodding"

Leaving aside whether any of the response to this post could properly be considered "venom" (I suppose some of it is a bit more strong than it should be) you are NAIVELY unaware of the fact that you may have brought this 'venom' upon yourself.

To be sure, if one where to point out actual flaws in a given model/theory or question aspects of it, others should listen attentively and address them.

...that is *IF* they are good questions and actual flaws.

What you have done is string together a series of poor examples and perceived flaws that are basically a waste of time and only serve to confuse the issue. They are not legitimate criticism.

That is why you are receiving such "venom" because you are negating your own premise, and causing harm to the world at large by perpetuating ignorance.

If you were actually interested in establishing a valid dialogue of the merits and flaws you would not be confusing it by bring in red-herrings and piss-poor examples.

I'm sure you would feel somewhat aghast if you noticed someone espousing very poor economic ideas. To be sure they are entitled to their ideas, and to speak them, and to a polite response...but if their ideas were irresponsible and flawed and this were posting them on the internet where others might see them and be misled by them, I think you would have a hard time not responding and trying to correct them...perhaps a bit heatedly.

We are all only human after all...and cannot help being a bit upset when we see people sowing what we perceive as misinformation.

Let me turn this around on you then and ask why you have not responded to the ACTUAL well thought out and solid criticism to YOUR views.

What's the point of complaining that you are "catching flack" for your views when you cannot validate them? Should you NOT catch some "flack" for having invalid views? I don't think it's unreasonable to say that perhaps you should (within limits of course).

This is an extremely insightful post. My apologies if all your posts are this insightful, because I've only just come across your site. I'm interested in republishing it in www.onlineopinion.com.au, or at least a 2000 word version. Can't see an email contact for you so wondered if you could email me graham.young@onlineopinion.com.au

As the anonymous poster who agreed with you earlier and not the most recent "anonymous" who says we are all human after all, as if there was some deep meaning in such folksiness, I second the opinion of Mr. Young.And you know you've done good by the nature of all the nuts that have come out to wave "naive" signs.Causing harm to the world at large? That's naivety on a shining shingle.

Actually, Eric has tried to respond, over at Novella's blog Neurologica. It's more of the same; basically his main concern is an argument from incredulity, and he's got a badly flawed mental caricature of science and scientists, and too much confidence in his poor knowledge of the facts he's trying to discuss, but at least he's trying...should shouldn't get beat up for not.

Dear Eric (I might have said Dr (Prof, His Excellency, etc) Falkenstein, but I regret that I don't know the appropriate honorific and I suspect that you prefer the informality anyway. Forgive.)I was impressed with your views (really!), but not in all connections convinced; the part that worries me is that the more I errr... "knew" of a subject, the less cogent your views seemed to me. I should love to go into your entire essay in detail but I am so rushed that I will hate myself when I have done. So will some others no doubt. However, in the unlikely event that you care a Hershey Kiss one way or the other, feel welcome to call me on anything I say. The following are not in any way structured, but random points that I perceived you to have made here and there. Forgive again, and forebear, especially where I improperly ascribe inappropriate views. Science. There is little point to defining it here because there are too many definitions, mainly too incoherent to be wrong. Popper for example was far better at selling a point of view than constructing a sound one. Possibly that came from never having had to do any honest lab work or experimental design. His deviation from the Vienna school was neither very creative nor compelling. He apparently hoped to destroy induction, but he might as well thought of killing time. Induction both outlived him and survived in his work in the form of unstated assumptions. His principle of falsification is almost as self contradictory as Derrida's deconstructionism, which he hesitated to apply to his own stuff. So I propose this (rather, fairly, sort of, vague) definition for my (our?) current purposes. Science is the (preferably systematic) activity of (constructing, discovering, and) selecting the strongest (most nearly working, most "useful") hypothesis available at any given stage, concerning themes at issue. Notice that it is practically intrinsically impossible ever to justify the assertion that you have included the "true, correct" hypothesis in the set under consideration, or even that you have included ANY hypothesis that is meaningful in terms of the genuinely true empirical situation ("reality", if you like). That process, or activity, intrinsically rather than formally, includes discussion, synthesis, reserved judgment and even (horrors) disagreement. Even among scientists. Especially among scientists -- if they are real scientists. Note however, that being a scientist and understanding a damn about such fundamentals are very different things. In fact to some extent they almost are opposites. Youngsters do science. Oldsters worry about what science is once they have burnt out and reached the infamous and (insufficiently) dreaded philosopause. So it is no good discussing science with most of the people doing science. They are too busy. Some of them remain too busy ever to reach the philosopause.None the less, the biggest single nit (or more appetisingly, bone) I have to pick, is your tendency to speak of scientists who apparently unconditionally defend illogic to beyond the death of the flogged horse. Now, some of them may believe in such things, I have met the like, (but actually most of those with whom I have consorted were eagerly willing to discuss, speculate and argue when away from the laboratory bench, where they had responsibilities too acute to permit them to risk discussion) but read what I said about the youngsters, or young fogies if you prefer. Consider what you said about theorising about dark matter (and the same could apply about most of the other fields out near the fringes where sane scientists fear to tread for fear of making a discovery). I quote: " It's like saying X=7, but when you measure X=9, you simply say there is an extra '2' of 'dark X'."************...

Mttr mttrr... Let's see whether this works...-------------Damned right! Extra over what? Over what you had expected. What had you expected? Concordance with the strongest extant working hypothesis. What had you found? Discordance! Oh dear! (Or more appropriately among the winners: "Yippeeeeeeeee!!!!!") How big was the discordance, and in what direction and context? If we had precious little precision so far (Like in the days of Tycho Brahe) then you might simply go on improving precision to the point that you can develop more coherent hypotheses (Einstein's precession of Mercury would have been pretty meaningless in the light of the work of Copernicus!) If otoh, we had something that we had described to pretty good precision and predictability, then we could make our predictions of discrepancies to establish new hypotheses; send out Eddington to observe an eclipse or something, and Big Bang! You have a general relativity and not an army in sight! Or you could get some funny results in your bookkeeping. Funny? What does that mean? It means that things don't balance, right? By how much? Would you believe by how much you were wrong? By as much as something that you had not allowed for? Go and read up how they discovered Neptune. The sillies! Or the Neutrino. The mystics! Or quantum spin. The dizzies! Or N-rays. The Nice people. Or cold fusion. The pioneers! Or...Notice that in each case (most of them in that list anyway) if the discrepancy had failed to match the subsequent discovery, there would have been more work to do. (There practically always was more eventually, right? Was that good or bad? Was it science?) And if the discrepancy was in the wrong direction, or just too stubborn, then what do you do? You consider an alternative. Any alternative that remains proof against your observations and predictions, and retains its explanatory and predictive power and parsimony. Including throwing Newton to the wolves. Would you believe, Eric, that from decades ago I have been reading proposals to dump Newton and Einstein in favour of this that or t'other that so far has not worked out? How silly to try things that don't work out! Those so-called scientists who made the proposals should be flogged in public for their boondoggles! Or was that the guys who stuck to Newton & co.? Well, whichever it was...Was it Keynes who said: "When the facts change sir, I change my mind. What do you do?"2X "Dark X"??? Possibly. X means... what? What does X mean when YOU use the term Eric? Where I come from it is an unknown. Dark? In this context it means that no one has seen it. Have YOU seen it?? Was it proposed as an explanation? Definitely not; it was measured as a discrepancy in terms of the existing observations, the pitifully difficult and sparse observations. Hey! If Newton (well, Einstein if you want to be really picky) was right, then SO many kg of dark X mass THERE could account for it. Now what sort of mass could that be? Axions? Neotrinos? WIMPs? Black dwarfs? Which was it Eric? Everyone else was silly, right? Or what about those who said: "Hmmm... now suppose Newton was wrong, then how much and when?" or maybe: "Hmmm... now suppose Newton was right, but there is another force, then...?" What about them Eric? Are they stupid to imagine either of the two classes of cases?Me? I just look at the arithmetic. "2X hmmm?" And I think. A little.Sometimes.Too little, no doubt.As for Darwinism, Eric, I am sorry to say that you are so far out of your ballpark that you simply are not coherent. For one thing, to get mixed up between Darwinism as she is spoke and what Darwin said is about as sensible as to criticise extant physical theory in terms of Galileo's ideas. Darwin (like Galileo) was great. Precognitive he was not! Should he have been? We should respect him, even revisit him perhaps, but we don't have to take him for Gospel.

Crwwwwth! What do you guys do if you have smething to say? Here I was only clearing my throat, and...

Anyway herewith the last anon.==========You know Eric, there are, as I have been saying for decades, certain subjects that in concept are so terribly simple that any simp takes one look and thinks he understands, but that in their development are so treacherously complex that the real pro has long since given up being embarrassed when he makes a booboo. One example is probability theory (and accordingly statistics). Another is Darwinism. For instance, you speak of Punk eek. It involved nothing truly new (as I am about to point out, in case you were drawing breath for a sardonic "AAAHAAAH!") although it did have the merit of stirring a pot that need a bit of a stir (in my case anyway). I well remember first reading the famous paper on the snails in Lake Turkana, and being duly baffled, till I saw the periods they were talking about for each of their events... 5000 to 50000 years!!! In situations of intense selection! That was "abrupt"??? Just go back and compare modern DOGS with those of 5000 years ago. (And don't bother to come burbling about artificial selection either before you do some serious study of the history of the breeds and their origins! No sense thrusting that foot even deeper in!) And as for speciation, go and read up on what a species is (or what a species are, actually!) THEN come back and talk about speciation. You could find some good, readable stuff at talk.origins. Also examples of speciation in appropriate contexts. But I said that punctuated equilibrium had it merits, right? Right. And then I trashed it, right? Not quite right. I don't know what it did for other biologists, but for me it opened my eyes to the smug way in which I had closed my eyes, not to periods without evolution (by definition there is no meaningful way to have such things in living, active populations) but to periods of relatively little or unobvious change between events or changed directions of adaptation. For quite obvious reasons (they should have been obvious, which is why I felt such a fool once my nose was rubbed in it!) such periods commonly (not necessarily) are longer than periods of change or radiation, which is why the changes seem abrupt in the fossil record. Darwinism (in its various transformations as it has advanced) is pervasive in biology by its nature. It also is one of the fundamental philosophical principles of biology, and that is why it is pervasive. Few biologists understand it properly and almost by definition non-biologists are not equipped to understand it; by understanding it to any extent you become a biologist almost to a matching extent. And to the extent that in demonstrating your mastery of the field, you make a cowpat out of a sows ear, you demonstrate how far you have failed to become a biologist by that Royal Road. Economics is better. That is a far safer field. No one EXPECTS you to make substantial predictions! (How am I doing as an instant economist, Eric?)So watch it Eric. For you to speak about branches of science outside your field of expertise is excellent; I do it all the time. People hate me for it. Even some scientists. Cross fertilisation and interdisciplinary thought and all that. Consider how Watson for example didn't know diddly about X-ray diffraction when he and Crick began work on nucleic acids, and see what they started! But when it comes to making pratfalls when sounding forth, leave that to the journalists in their superiority. Leaving their droppings for others to sniff at and moving on too fast for meaningful criticism to catch up with them is their smug speciality.And you and I can do no better than admire from a distance.

I think 'the argument of incredulity' could apply to both sides. I don't find the evolution of all species given piecemeal, adaptive, random mututations, can create vastly new tissues and organisms. That's my incredulity. Others are incredulous that everything was not created via this mechanism. That's their incredulity. Neither of us present probabilities. The only real numbers we have are when life started, say hundreds of millions of years, that this happened. The state space for the protoorganisms, the intermediate adaptive phenotypic mutations or combinations, the number of non-adaptive, or non-successful, phenotypic mutations, no one knows. Both sides do not have numbers, and are relying on intuition. I think the 'we know time + existing mechanisms can explain everything' argument presumes a scalability that is yet unproven. Many solutions aren't scalable, so I don't take it for granted.

jon: well, you mention several points, but seem to suggest to leave evolution alone, because I'm making errors supposedly refuted over at Talk Origins. I have read much of that site, and admit I don't understand everything, but what I do understand seems not nearly as convincing as the authors think. So I note several well-known issues that the conventional wisdom sees as creationist drivel. I don't have their endgame, but I find many of their criticisms highlight interesting inadequacies to the standard theories. As an unpaid blogger, I'm just speaking my mind, and don't feel obligated to peer review these opinions. Many seem to think any criticism of evolution merely helps a meta argument related to God, and so label all such criticism as outside the pale. I don't care.

As per puzzles generating advances, sometimes they do (such as Neptune, or Rutheford seeing electrons bounce back (thus discovering the nature of the atom nucleus)). But in the case of dark matter, or applying asteroid corrections to every planet in the solar system, these are often merely persistent puzzles, and have not generated successful new models that have generated new insights. We just have patches, epicycles, and there are interesting because they suggest something is missing. Until we find the missing theory, we shouldn't be really 'happy' about these lacunae. It's science, sure, but the probability that 'epicycles' generate new successful theories is not so high, and often they stay epicycles, though we get used to them.

I have not read "Icons of Evolution". I have seen some videos with Wells, and read some of his writings, however. But, I think you are going in a strained direction. Many who criticized Behe highlighted this was already refuted via the refutaton of Paley's argument via Darwin's complexity of the eye. Then, they do a lot of hand waving about things that could have happened, QED. I think Behe highlighted the tight constraints on mutation implied by the constellation of functionality at the intracellular, protein, level. This makes the probability of a local fitness maxima that much more likely, making these little changes much less fruitful.

So, I'm thinking there's another way, though I'm clueless as to what it might be.

Clue to the "other way." Incremental trial and error. Beneficial uses can be made by life forms of what appear to be accidental mutations, and it's not inconceivable that life forms found ways early on to effect the mutation process through the incremental application of deliberate trials and "intelligent" reactions to any sensed consequences. No necessity for goals or purposes involved other than to simply poke around because something interesting often seemed to happen and therefor was expected to result from the poking or probing. Probing being the first mechanism arguably developed by life forms that allowed their eventual survival.

Eric - for someone who wants to be mechanistic and see concrete examples, you might be wise to steer clear of Behe - every one of his examples he has given as "impossible" or "constrained" has subsequently been found to occur in nature, or be otherwise refuted. The hand-waving you decry is irrelevant, we have hard data refuting most, if not all of his and Well's specific claims.The constraints you refer to are also looser in many respects than most biologists used to believe - you might be interested to read about Susan Lindquist's work on chaperones.As to whether we know all about how variation is generated to overcome local maxima etc, obviously we do not. This is a subject of active research, otherwise there would be no working evolutionary biologists. If someone were to come up with *evidence* for such a mechanism, such as those who have proposed contingency genes (basically mutational hotspots which exhibit increased variation under stress) - they would be lauded, not vilified.The reason you have attracted such vigorous responses is that you are repeating old canards and postulating the requirement for novel mechanisms with no evidence for their neccessity.

The problem with your "you can't get there from here" argument, Eric, is that you're asserting too much from it without evidence. You need examples. But when the likes of Behe or Dembski offer them, reality smacks them down hard. On the side of science, we have observations, experiments and models showing that the kinds of adaptations Behe & Co. say can't happen, can and do. I'm talking direct observation here. We also see functional intermediates and some very interesting models, all of which are going toward the plausibility of evolution scaling from the relatively small to the grand. And conversely, when Behe & Co. are asked to provide examples of discrete barriers to such scalability, to describe and support mechanisms, they fail repeatedly.

You almost seem to be arguing the Creationist stance (note to Dave c: I'm pretty sure Eric stated he's a nonbeliever earlier...?) that the concept can't be accepted until we know every single link in the chain--say, every mutational and phenotyic step from eyespot to camera eye. If that's so, we may as well drop the conversation. We'll never be able to even approach that level of resolution in real-world material data (though it's just barely possible we might in simulation.)

But if you are simply looking for help grasping the plausibility, then again, I cannot recommend enough the books I recommended earlier, and other good recent books you can find readily recommended by Novella and other bloggers. I think you will find the "leveraging" and "creative recycling" of the Evo-Devo field especially interesting. There is much more going to the plausibility than you think, and the gaps are being plugged daily. And we KNOW there is room in them for new mechanisms, and indeed suspect we'll find some (in some ways that's what Evo-Devo IS) so I wouldn't worry quite so much about closed-minded science-monks. We just need evidence, and it should lie in the places we're looking.

If I was to tell you that I am not an economist but I don't think that the law of supply and demand can possibly explain macroeconomics and is obviously flawed but you have to accept it or be ostracized from the circle of economists with their current cult-like devotion to this mistaken notion. What would you think?

jaranth: the counters to Behe seem to have a lot of gaps. Dawkins o referred to a 70 year old argument to counter Behe, and not taking new arguments seriously by categorizing them with familiar flawed arguments of the past is lazy and not convincing to anyone but those predisposed to his endgame. He has a lot of readers, so he can coast on this rhetorical style until he's dead, but it's pathetic. Look on Talk Logic about the flagellum, and it's a hypothetical. The potential solution is just as unpersuasive to the other side as Behe's incredulity that a flagellum could transport all these different amino acids within all these proteins with all their logistical protein structures via simple mutations. Or take the intermediate forms given as 'proof' that evolution happens just like in the Origin of Species (also, remember to note that subtitle is now verboten!) , but these could just be like saying the fact we have seals, whales, fish, and foxes, proves 'the' evolutionary mechanism, because of homologies. I still think the mechanism needs probabilities applied to state spaces, for mutations, fitness, etc. If I saw actual numbers, I would be convinced, but all I see are anecdotes, vague fossils that look like intermediate species, but could be like platypuses, as any two extant species today has extant potentially intermediate species based on 'homologies'. No numbers, so I'm a skeptic (supposedly it is good if skeptical of 'cranks' or anything vaguely tinged by religion, not if skeptical of 'conventional wisdom' in academia--hurray for free thinking!).

As per dismissing supply and demand, go ahead. If you do, no economist will write book denouncing you. These are actually malleable enough constructs to give one a lot of leeway, so whether you are a Marxist or Free marketer, these tools are useful, and if you ignore them, that's fine too. There's some useful logic, and empirical justification for them, however, so if you merely dismiss them your arguments will need some extra oomph to not be knocked down very easily. Economics does not have the religious overtones of evolutionary biology that creates similar defensiveness, though we have our own artificial constructs of what is considered 'beyond the pale', which I also think is flawed.

The bottom line is that I do know some areas of science very well, as well as anyone in the world, such as stochastic discount factors manifesting risk, or predicting corporate default rates. I see how certain experts are charlatans, use excessive formalism, or flawed analogies to gain credibility. So I'm not awed by an esteemed professor when he appears to be making a weak argument. Popular scientific beliefs are often very wrong, as anyone who has read history knows.

I'm happy to think that for many issues, we (humans) are simply too stupid to generate a correct theory. To think what it took to generate Newtonian mechanics, it may take 10x to derive the actual laws of the universe, or business cycles. Our best theories aren't correct merely because they are our best. I'm OK with that, because for most of this kind of science, we don't have to have an implicit opinion (eg, my explanation for the EPR paradox, is unnecessary for my or my government's tasks).

And so again, I recommend you do some good reading. You talk a lot about numbers, but you also talk quite naively about a lot of other facets of evolutionary theory and the debate between scientists and religious apologists. What you’re claiming isn’t understood or understandable very often IS.

Given your profession, I can certainly understand your interest in numbers. But again, this is argument from incredulity, and again, where you have incredulity, biologists have evidence and plausibility. There are a LOT of numbers in evolutionary biology, including some going to precisely what you want. And as I’ve already pointed out, these are areas where research IS being done. We’d love to have lots of the kind of data you talk about, and computers are going to help (and have been helping) a lot with this. But this is in part a historical science, so we know it can never be complete. Far worse is the fact that many of these probabilities will be impossible to establish by their very nature—we can’t always know the boundaries. How many possible solutions are there to a given evolutionary problem?

As for supply and demand…I assume you were referring to someone else…?

The last post is the re-emergence of offensive personalised comment that lowers the quality of the blog. If the poster thinks they are a scientist they can post an argument. Jaranath has said science is not his/her occupation but their blogs show politeness is.

Aren't you the one that accused Eric of causing harm to the world at large, albeit politely? And where were you when another faker referred to his ass and said he was a shame to his profession because of a clearly Christian bias? Quality is measured by the politeness of fools? Mmmkay.

"There's some useful logic, and empirical justification for them, however, so if you merely dismiss them your arguments will need some extra oomph to not be knocked down very easily."OK. Who will be the judge as to the strength of the arguments?

"Economics does not have the religious overtones of evolutionary biology that creates similar defensiveness, though we have our own artificial constructs of what is considered 'beyond the pale', which I also think is flawed."

Interesting referral to religion and defensiveness here. Not sure what you mean by it. Evolution is a well established theory. If a theory came around that explained findings that it can't, and make accurate predictions that cannot be made by evolution, then it would be superseded, just like Newtonian mechanics was superseded by relativity theory.

Hello Eric,Look, sorry, I didn't mean to come across all mean, but obviously I was writing (a) fast (which I do so badly that I periodically swear never to do it again) and (b) addressing mostly the points I had problems with. Maybe I should use lots more emoticons, but that takes too long.First lets deal with your asteroids. A) They are not all asteroids, but can be comets and all sorts of classes of space junk. Let's just call them OOs (orbiting objects) in this conversation. B) You quote wide ranges of "authorities" as supporting documentation. Some are substantial, but others either are fringe or amateurs doing handwaving. C) Your objection sounded as though you were criticising a scientific theme; it is nothing of the kind. The various examples you give are different kinds of event with different kinds of effect, alternatives to various kinds of explanations, quoted in various contexts, and from various authorities as I mentioned.D) In your criticism you give the impression that what you are shooting down is the "verdict of science" (my expression, not yours) concerning the strongest extant hypothesis for all events in that class of outstanding problems. It is nothing of the kind. Some of the examples are the mildest or wildest of speculation, the kind of thing that might get bandied about during a coffee break. Several of them I would give short shrift even then. Some are too vague even to criticise coherently. For example we know very well that every single major body in the solar system, down to football size, has undergone multiple collisions in the last few billion years. Although there are a lot of I's to cross and t's to dot, there is pretty broad agreement that all the planets formed by accretion of smaller objects. This view goes back some three centuries or so, and it has been growing in detail in recent decades. If you would like to be lynched don't bother to oppose this theory in the presence of astronomers; they would hardly yawn. On the other hand, the process amounts to OO collision on a gigantic scale. Why then do we have so many planets in so many orbits in nearly the same ecliptic and same sense of rotation? This is not as simple a question as it sounds, but it comes down to a combination of statistics and conservation of angular momentum. The statistical aspect implies that there should be deviations in orbit and obliquity, sometimes in fact because of one or more major OO collisions. We even have been privileged to see minor collisions quite recently. Remember Jupiter? Some of the examples were simply henwitted, such as the idea that OO collisions could have anything to do with the desiccation of Mars. Others, such as the creation of Luna, have been carefully motivated, analysed, and convincingly modelled. Proof? Of course not. Science does not prove. The job of science is not proof. But a little coherence is nice.

H$%^CK and BL*&^%$T! This time I kept it under 4K and it seems to have padded it out or something.Sorry, back to the serialising. Darwinism next, though briefly!

Evolution..." I don't find the evolution of all species given piecemeal, adaptive, random mututations, can create vastly new tissues and organisms. That's my incredulity. Others are incredulous that everything was not created via this mechanism. That's their incredulity."Go into any Genetics, Biochemistry, Palaeontology, or vanilla Darwinism department in any university department and try to get a hearing either for or against Darwinism on the basis of credulity or incredulity. Still no lynching, but what would happen would be rather as though you (well, let's say I, who to this day cannot understand money (really!!!)) had done the equivalent in an Economics department, tolerantly explaining that I had read all the popular books and listened to all the popular TV panel discussions (I haven't actually) and they were all wrong (I bet they are!  ). What do you suppose they would say? Are you under the impression they would take up arms for or against me? Or would they smile kindly and suggest that I go and bother professor Blank, who really would find my views very interesting, but PLEASE don't say who had sent me?"Neither of us present probabilities." We don't huh? Duh! Tell me, Eric, just HOW would you express some of these probabilities? YOU don't need ME to tell you that statistics works strictly on GIGO? On the other hand, if you read some of the pro papers on evolution or any other branch of Darwinism, you will find a darned sight more maths than most of the graduate population wants anything to do with. Now, not to send you any more serialised hoots, and to get back to work, I'll cut it here for tonight, and assume that you will henceforth get your Darwinism from source, instead of pre-digested, but if you would like some helpful remarks on troubled questions, feel welcome to ask. I'll look in occasionally.All the best,

jon: First, I must say 'all the best' is a nice signature of good will.

I think it is important to note my problem is not with 'Darwinism' in general, I think something within this definition explains life, but given I don't believe in miracles, I don't find this 'theory' very powerful. The mechanism examples are generally microevolution, and then a wave of the hand, and speciation, movement of complex proteins and their intricate logistic structures into a different and more complex functionality. Now, playing with E. Coli or fruit flies in the lab should have produced some examples here, but instead merely degradative ones (or trivial things like legs where eyes are). It would be very convincing to see the creation of new complex functionality.

Think about the placebo effect. At almost any stage, one can make marginal improvements in patients via placebos. That's been well documented, a fact. Yet, it does not imply one can count on placebos to fix a blocked heart artery. Many economic experiments work differently when done with $10 payments given to university students, as opposed to affecting people's wages. Or that the optimal process for discerning patterns with 100 observations is different than when examining 1MM observations. Many simple algorithms don't scale.

My problem is not 'Darwinism', but rather our current proposed mechanisms, which seem either inadequate or vague. The empirical fact of punctuated equilibrium, and the unconvincing argument this is merely the accumulation of many small fitness modifications just like our malarial defense, tells me there's a problem here. If as you admit, actual numbers are hard to generate, you should understand the reasonableness for skepticism, because different numbers generate different probabilities, and science is all about probabilities, not possibilities. The mechanisms highlighted still have the famous 'a miracle happens' stage, but here the miracle is 'millions of years is so long this must have happened' as opposed to 'God did it'. Either way, I think the specific theories presented for explaining the diversity and complexity of life is in a pretty poor state, and often presented in a very misleading way.

Lastly, evolution is very unique, in that it is one theory where 99.9% of all academics believe in it, yet popular science writers spend a lot of time defending it. That should strike one as strange. Methinks they protest too much, highlighting their insecurity. They know their theory is very incomplete, but can't stand the thought God, or perhaps the politics correlated with religious people, will gain popularity. They may have a point, but it makes for disingenuous argumentation. Nonetheless, Dawkins and Myers have rather strong animosity for those they assert are saying 2+2=5, which is not a consistent response.

Whoa there Eric, you are beginning to exhibit the characteristics of the deliberately ignorant where evolution is concerned. Various posters, silly or not so silly, have offered advice, books to read, etc., and you persist in pretending there simply are no answers out there to the questions you have legitimately raised. Your persistent stance of disbelief that any of this will change your opinions or add to the state of your knowledge means you either have a separate agenda to promote (like maybe a book you wrote) or simply enjoy the present state of your ignorance so much that you fear to disturb its equilibrium.

This piece would have been more accurately titled "Some economists don't know shit about science." In the one area I know well, evolutionary biology, it's full of misconceptions and misrepresentations. Were I to write as much ignorant B.S. about economics or finance as Falkenstein has about evolution I'd be rightly laughed at by him. Well, I'm laughing at him. (And for the record, I teach a course in evolutionary modeling in a biology department, and also have modeled markets to drive trading for hedge funds for over 15 years.)

Darwin anticipated finding all sorts of intermediate forms in evolution, but these are the exception, not the rule. Indeed, Gould's punctuated equilibrium theory was first seen as untrue, but then, a minor change in emphasis that Darwin's theory allowed all the time. There is much effort to show Darwin did not reject sudden changes, but clearly the Origin of Species emphasized the smaller steps. One can argue that 'sudden' in geological time is long in generations, but nonetheless, it's a major change in emphasis. The scientists like to whitewash these debates because they are scared to death of looking uncertain to Bible thumpers.

Intermediate fossil forms are not the exception. At relatively high taxonomic levels there are excellent series of fossils showing the transition of tetrapod ancestors from water to land, of whale ancestors to the water, of reptiles to mammals, and so on.

At the species level transitional fossils are rarer, though by no means absent, and Eldredge and Gould's punctuated equilibria proposal was devised to account for that. The core argument they made was that in contrast to Darwin's original view, most speciation is allopatric rather than sympatric. That is, E&G proposed that most speciation occurs in small isolated populations, taking only thousands rather than tens or hundreds of thousands of generations because the population is small. Later, when the new species over-runs the larger territory occupied by its ancestral population it gives the (geologic) impression of sudden appearance.

The fossil sequence showing the speciation event is difficult to find precisely because it occurred in a small and isolated population. Taphonomic considerations alone suggest deposition of such sequences would be rare, and then paleontologists actually finding the deposits infrequent. Nevertheless, in their original 1972 paper Eldredge and Gould provided data on two fossil series, one from Eldredge's work on trilobites and one from Gould's on snails, illustrating the phenomenon.

However, in no sense did Eldredge and Gould propose a non-Darwinian view of "sudden" speciation. The fossil data they provided showed the incremental change that is the hallmark of Darwinian evolution by natural selection. They did not hypothesize large steps, they hypothesized (relatively) rapid sequences of small steps. Hence the impression given in your OP, and in particular your use of the phrase "sudden changes" and your mention of the Origin emphasizing "the smaller steps," misrepresents punctuated equilibria and promulgates a false impression of the state of affairs.

Neither of you however are willing to include biologically directed mutation in your scenarios. One thinks it will lessen the possibility of theistic role in the process and the other thinks that somehow it will increase that possibility, once you concede that any sort of direction is in play.

"Take the 'evidence' for evolution, which has been assumed overwhelming by conventional scientific opinion for over a century, "

Not quite true, I'd said. Not until the Modern Evolutionary Synthesis (wiki it) has there been such opinion. Prior to that, it was the usual helter-skelter science, giong first one way then another, while Spencer and the Social Darwinists made hay out of nothing.

Just a few items. Anon (one of you anyway. You are legion aren't you? Why not pick a distinct label to unfuse the confusion?)Directed mutation.

That was an *elephant* I tripped over? I thought it was a coffee table.I have no definitive views on Darwinism (plenty of plain ones of course, but who hasn't? Even though a lot of embarrassingly ignorant people represent their own views as definitive, even when they aren't even meaningful.) However, such as my views are, they are strongly tinged with confidence in information theory, thermodynamics, causality (though not determinism for most precise purposes) and similarly unimaginative mental constraints.The operative word, "directed", as used by most of the most strongly partisan contenders in this debate, seems to me unacceptable on the principle that exceptional claims require exceptional evidence. To my mind any evidence that does not demonstrate very strong evidence for a causal informational connection between the environmental effects on the organism, and the nature of the modification to the genome, hasn't got to first base. It would amount to a demand that we accept a mystical (non-)explanation. That does not mean that it would be false, of course, but it certainly would rule it out of the scientific process as we know it. Even if we then did try a lot of experiments and got consistently clear evidence of directedness in mutation, thereby having to accept that it is a real phenomenon (which is by no means clearly the case) we simply would have to accept that there is room for investigation (and not only is that the case, but investigation germane to the issue, even if not directed at that issue specifically, is constantly in progress). Now, ask yourself: If someone dunks a bacterium into lactose as its only source of carbon, what part of it says: "Oh my goodness! Lactose huh? Lemme see... suppose I change this base pair down here around; that should change my sucrase into a lactase! Hey it works! More sex here please!" My point? "Directedness" suggests some form of either anticipatory design (a la mouse trap) to react mechanically and causally to circumstances (e.g. "trigger moving means mouse: squash 'im!") or continuing Turing awareness of circumstances, appreciation of causes and of the choice of effective reactions, and the ability to apply those measures. That is a tall order. I give you serious odds that you will struggle to make a cogent case for anything of the kind in your common or garden E. coli. Populations are a little more powerful, though not all-powerful. Consider: Those lactose-conquering E. coli produced only a few surviving cells (two in the first experiment? Can't remember the details) that went forth to be fruitful and multiply. They did not do so by creating new genes; they had the makings from ancestors already. The reason that the main population were unable to chomp lactose is that their lactase gene was variously inhibited. What happened was that their lactase inhibiter gene got zapped. Genes get disabled all the time; it is one of the commonest effects of non-silent point mutations. $%^&*(I seem unable to answer a question in less than 4K char... More coming!

OK, more on directed elephants. It has been known for decades that various creatures when exposed to adverse situations increase their rate of mutation. It has been theorised (not unreasonably, I reckon) that this is a survival factor favouring currently effective genes and inviting possibly new effective genes when hitherto effective genes no longer bring home the bacon. So we have a population with nothing to eat, and a couple of mutations, possibly only two out of many that would have been equally or more effective, either of which would suffice, and when challenged, a large culture of the bacterium produces surviving lines with particular mutations? Amazing! Must be directed, hm? No other mutations were produced, were they? Now, a question that Aesop might have asked: "What happened to all those cells whose lactase genes got zapped by the directed mutation mechanism instead?" or even: "Has anyone repeated the experiment with E. coli with that lactase gene deleted?" For all I know all that has already been done. Why don't I know about it? One reason is that that coffee table elephant has not cocked a leg against my ankle. I am not impressed enough to keep an eye on the field. I don't think there is much to it. Could I be wrong? MEEEE!?? Don't blaspheme! Have I EVER been wrong in matters of science before? Um, actually I have. When that happened, guess what? I didn't roll over and die. I didn't vituperate much except for the occasional "Well F...an my aunt Charlie with a Lonomia caterpillar!" Why should I? I love intellectually stimulating surprises. Now, in these respects and in the light of these circumstances, I suspect that most evolutionists (professional Darwinists or whatever you prefer to call them) would react similarly to the directed mutation idea, but might, depending on their field of study, be interested in following up the work on stress and mutation. Many are doing just that, I believe. Remember too that adaptation by mutation is not a random process, and Darwinists do not think it is; haven't for yonks and yonks, if ever. The mutations too, are not only not truly random (there are sources of bias, none that I can remember offhand, except for constraints on protein transcription and so on) but (non-)randomness there is not a very exciting field. But demonstration of deviation from randomness is far from demonstration of directedness. After all, how much work was put into the research to demonstrate that those genes that got zapped and created the strains that survived, got zapped any more frequently than genes for enabling the digestion of trehalose or cellulose? We only SAW the lactose hydrolytic genes, because they were the ones being looked for.

OH, and in case I didn't make it clear about:"Jon, what are the probabilities that biologically directed mutation will soon become a major field of study by evolutionary biologists?"

I would say: Don't bet any family jewels on it. They might very reasonably investigate some effects that emerge during such research, but not as anything that I for one would regard as "directed mutation".

If you would have wanted a meaningful figure for that probability, please formulate the question suitably and suggest an appropriate line of research.

When confronted with evidence counter to your assertions:"The venom generated by questioning the evolutionary mechanism highlights this is now a 'taboo' subject"

In reply to Orac:"orac: the crank ideas are not debates. I don't know anyone, personally, who believes in those examples you give, though I know some people believe them. I think you can distinguish between crackpot ideas, as these are held by such a small number of people with little credibility, they don't matter."

Herein lies the crux of the problem: your ideas about evolution are equivalent to crank ideas, in this case. So you're being treated as such even if you can't "distinguish between [your own] crackpot ideas" and actual science. That you see the reaction as 'venom' should have been your first clue. It certainly was ours. The "little credibility", in this argument, is your own.

You've been called out as a pot calling the kettle black and you need to be man enough, or scientist enough, to admit you were wrong and just as ignorant of the science in this instance as you've accused others of being.

Eric, you say:"...playing with E. Coli or fruit flies in the lab should have produced some examples here, but instead merely degradative ones (or trivial things like legs where eyes are). It would be very convincing to see the creation of new complex functionality."

" trivial things like legs where eyes are" Trivial??? You blaspheme, Squire!" Those were some of the effects that led to some of the work on Hox structures! They led some of the most fundamental biological discoveries in the metazoan ever!I spoke a while ago of having been wrong; ME! One of the things I was wrong about was that I didn't believe in the idea that invertebrates and chordates were basically the same body plan inverted, so that their Hox genes might be interchangeable. And chase a gum tree up me, it turned out that they were!!!If you can think of a similarly earth-shaking scientific discovery in economics, tell me aaaaallll about it! It rivals the identification of mitochondria as honest to goodness bacteria. (Mind you, that one I believed from pretty well when it first was published.)As for discovering something really new, like flying pigs or honest politicians, noooo problem! Just give us Madagascar and a few tens of millions of years. (Um, well let's not be greedy... scratch the politician idea. Would you settle for Triffids?) Get the idea Eric? Your demand is internally inconsistent. And as for transitional forms, RBH was too gentle. Eric, EVERY fossil except for those that happened to be the last of their lines, leaving no descendents, was a transitional form or "missing link" if you like: follow their ancestry far enough back and you find different creatures. Follow it far enough forward and you find possibly many things different. How in any case, are you going to choose a missing link between two forms? Take the one in the middle, halfway along? What then is the link between the link and the original two species? OK, halve the gap on each side. Where does this process take you? You wind up with a complete genealogy. Only palaeontology forbids... Darwinism fails the challenge.If you look on line you might find the text of "Mr Belloc Objects" by H.G. Wells. More than eighty years ago he pointed that out. Clever boy, our Herbert George...

Jon, you don't need an anticipatory design to accommodate a capacity for direction, nor do you need to choose the narrowest definition of direction to denigrate the concept. All you may need for "direction" is an anticipatory problem solving algorithm, and there is "evidence" (again broadly speaking) that cells are replete with such algorithmic systems.

Elephantman,If I was too narrow, that were a grievous fault, though inadvertent. However, I do not see what you mean in this context. I thought I had covered the idea of "anticipatory problem solving algorithm" (as in mousetrap) but perhaps I misunderstand. In fact I don't really know what you mean by "a capacity for direction". Would you care to elaborate?

You speak of ""evidence" (again broadly speaking)"? Well, that is OK; this is not a refereed thesis, but an informal discussion. But could you say a bit more (still informally) about the nature of some of the "algorithmic systems" that cells are replete with, and what they have to do with how directional mutation might work?Cheerio,

Jon, you wrote: ?My point? "Directedness" suggests some form of either anticipatory design (a la mouse trap) to react mechanically and causally to circumstances (e.g. "trigger moving means mouse: squash 'im!") or continuing Turing awareness of circumstances, appreciation of causes and of the choice of effective reactions, and the ability to apply those measures. That is a tall order. I give you serious odds that you will struggle to make a cogent case for anything of the kind in your common or garden E. coli."Maybe it's the anticipatory design phrase that was the craw sticker. And a capacity for direction exists in every organism capable of executing the simplest of trial and error functions - which is somewhat of a tautological observation since such a function is life's first necessity.And Jon, you know as well as I, if not more then, where to find such evidence. But try Lynn Margulis' "What is Life" if you haven't yet done so. Google Biologically Directed Mutation if you must, but of course you would have done so long ago if I know you.And disbelieve me if you choose, but I'm preparing a paper on this very subject, and not about to use this site for pre-publication purposes.

And a capacity for direction exists in every organism capable of executing the simplest of trial and error functions - which is somewhat of a tautological observation since such a function is life's first necessity.

But, of course, that individual organisms are capable of goal-directed behavior, with all that implies, in no way provides an argument for the proposition that evolution by mutations of genetic material and natural selection (a population process) is goal-directed, or that the variation generated by mutations is somehow guided in the light of population goals. It's pretty difficult (impossible so far) to demonstrate that the variation available in a population is correlated with selective "needs" or "goals," but that's the argument you must make.

Not at all. The only goals needed are purposive "hopes" for fulfillments of expectations in the shortest of incremental steps. And I expect you realize that the only terms we can employ for any description of these processes are necessarily metaphorical.

And population goals, if any, might be limited to needs or assessments such as more, less, enough, not enough or too many.

||I just find the mechanism as currently described insufficient, it's missing something, and advocates pretend like it works great, which I don't think is a good description of the theory.||

First, this a straw man. I don't know any evolutionary scientist that pretends what we know "works great". There are certainly gaps. Being reasonably confident those gaps are probably going to be explained by some natural mechanism and not a Harry Potter god is not pretending it works great. Geez.

Second, you, as an economist, are incredulous about a very complicated theory in biology that draws upon multiple lines of evidence that are not very easy to understand by non-biologists. Hmmm. Sure. Believe what you want. Knock yourself out.

But what would you think if a biologist said he was incredulous about this international trade stuff and it seems obvious to him that the route to prosperity is to close the borders and pursue a policy of "Juche" (as the north koreans would describe it). Everything he claims supports his view of economics comes from sources that sound a lot like North Korea.

You might think him a touch daft and point him to a few years of book learning.

Hi Elephantman,>... I'm preparing a paper on this very subject, and not about to use this site for pre-publication purposes.<Fair enough. If you wish to email me a copy for confidential comment, feel welcome, though I might not have the necessary opportunity to give it full attention before late Nov. (family commitments etc.) However, I doubt that my comments would be very constructive. Like RBH I find some of your remarks a little opaque, which suggests that you are currently in a state familiar to anyone who has been writing something out of the normal line: too deeply steeped in his own mode of thought and expression to realise how unfamiliar they sound to aliens. Been there. Bad experience. Of course, I may have the wrong impression. Hope so. >And a capacity for direction exists in every organism capable of executing the simplest of trial and error functions - which is somewhat of a tautological observation since such a function is life's first necessity.<

OK. No problem there. But what does that have to do with what for me is the REAL craw sticker; the: "um... what is this unfavourable circumstance? Which gene shall I twiddle? Which base pairs?" If there are no means for the organism to assess the existence and nature of the problem, and to select and apply a specific solution, then I do not understand how you are even to approach a the formulation of a hypothesis to apply. On the other hand, if this is NOT what you are proposing, then what is it that you are calling "directed mutation", and why? If these points are in your paper, then certainly I respect your reserve, but I don't see how we are to comment on the points.

Am I missing something? >Maybe it's the anticipatory design phrase that was the craw sticker.<Maybe, but for the nonce you have me stuck, for the aforestated reasons. >And Jon, you know as well as I, if not more then, where to find such evidence.<Not very likely. I haven't been working on it and you patently have. >But try Lynn Margulis' "What is Life" if you haven't yet done so.<I respect LM's work, with mild reservations on the emphatic and inclusive nature of her views. If I understood her correctly, she would regard a cow, with its rumen and other flora as "an organism". Well, I understand her point, but I am not really comfortable with what strikes me as a tenuous point. It is not exactly on the Gaia level, but still... Mind you, I do take a broad (and conceptually challenged), but mystified, view of what life is, but in my opinion the principle tails off into diluted meaningfulness as it become more inclusive.

>Google Biologically Directed Mutation if you must, but of course you would have done so long ago if I know you.< It seems that you do! :-) I checked on what seemed to be the state of play. Unfortunately, I still have no idea of where or in which direction your detailed interests lie. That rather crimps my style in terms of my scope for constructive comment. Also, do remember that I am no authority, not even a competent worker in the field.Sorry about that! Cheers, Jon

Hi Elephantman,Sorry, forgot to say, I have not read many of LM's books (family rationing and all that!) and "What is Life" is not one that I know. I am guessing at the line she takes in it, from other items she has written.Gp well,JR

Elephantman, you said to RBH i.a. >...the secret, if any, is to understand that all long term evolutionary progress results from the cumulative effects of short term biological strategies.<I could only even begin to take that seriously if we carefully make explicit what evolutionists take for granted:That short of species whose intellectual development has achieved high levels of indirect teleology, and mostly not even then, "evolutionary strategy" has nothing necessarily to do with conscious intention. (Understanding mechanisms deeply enough to do one thing with the intention of achieving something different, or even opposed to the direct objective. So far, as far as we know, Homo sapiens is the only one to reach the capability of an abstract understanding of information, algorithmic design, molecular biology, and genetics.) Now, I assume that you are very well familiar with that principle (give or take a few details of emphasis or context) but my difficulty is that if you do agree so far, then I do not understand where purposive directed mutation comes into it. I suppose you could say that a virus of one of the many types that insert genetic code into the host's genome could be said to do something of the type. There also are intriguing viruses that ride on the DNA of polyembryonic parasitoid wasps attacking caterpillars as symbionts, dying after having paralysed the host's immune system. Such systems are breathtaking to put it mildly, but in which respects are they convincing examples of "directed mutation" in accordance with some sort of evolutionary strategy? If I do not misunderstand you hopelessly, I do not see how to make sense of what you said to RBH. If I do misunderstand (I often do!) then unless the necessary explanation is part of your article, do you suppose that you could clarify our fog?

Jon, I appreciate that you found my reference to the metaphorical "secret of life" at least intriguing - rather than to reject it out of hand. I don't have time right now to give a detailed response, and can't promise such later. But my paper is precisely about the nature of short-term biological strategies. You will I hope concur that strategies are endemic to life, and perhaps consider my surmise that intention is a metaphor for strategic purpose (there I go again with this alien jargon). But I think you have drawn the wrong inference by the reference to evolutionary strategy. I do not imply that evolution itself is or has a grand strategy. It's life itself that is, for want of a better way to put it, a strategy (and grand indeed) of nature, a strategy "discovered" by nature for making its own choices. But these choice directed strategies are biological - goal seeking with no conception of the ultimacy of such a process.It's the nature of the seeking process devised by life and common to all its forms that I seek to elucidate.

Jon, pursuant to certain of your comments about purposive direction at perhaps the cellular level, look into work being done on this concept:

Preadaptive Evolution

"Preadaptive evolution" is a remarkable concept. Basically, it asserts that in some -- possibly many -- mutations, a useful response to an evolutionary challenge is "naturally" accompanied by useful responses to challenges that have not yet been posed to the life form in question. This prescience verges on the miraculous to the uninitiated, but mainstream biologists seem content to write the phenomenon off as merely good fortune -- like hitting two jackpots in a row on the same slot machine.

A good example of preadaptation occurs when bacteria are cultured in the presence of an antibiotic. Within a few weeks, they have evolved a resistance to that particular antibiotic. This well-known phenomenon is easily explained by evolution. However, often the newly evolved (or "adapted") bacteria are also resistant to several other antibiotics that work by different mechanisms. All of the multiple gene changes needed for the several different defense mechanisms are controlled by a single site on the same chromosome.

Elephantman,Some of your remarks are getting into fields and concepts that are undoubtedly intriguing and very important. They also are tantalising in that they deal with some very slippery concepts. I suspect that many anti-Darwinists fail to make a meal of them because they are meats too strong for infant digestions. (If you have read typical arguments from those quarters, you will know what I mean. Even Behe, who was unusually well-qualified among that crowd, came up with embarrassingly self-defeating theses. The fact that experts in the field chose to rub his nose in his own errors of fact, insight, and principle, may have been have been impressive to the uninitiated (in fact they included some very impressive tours de force, but never mind that) but in fact if none of them had said a word, the principle would have remained unshaken. Behe simply jumped head-first into a God-of-the-gaps bog, poor unimaginative sod! His friends should have sat down with him (or on him) till the feeling went away.) However I am uncertain to what degree you and I have major differences of opinion beyond semantics. Now, the question is whether with your time constraints you would find it useful to discuss the matter any further with a non-professional, and if you do, whether the others in this forum would prefer us to take it off line, or whether you would wish to do so anyway for reasons of confidentiality. If so, let me know and I'll give you an email address. Otherwise I'll prepare some remarks on what you have said so far.Till then,

Jon, I'm not sure if in referring to anti-Darwinists, you would expect them to chew on or instead chew up my conceptions, because I consider myself no more than a Darwinist with an auxiliary theory. Anti-Darwinists would do well to fear that it might be substantive.

Also, as in any such endeavor, one could do with a collaborator, but one could also be done in by such.Many the innocent struck with an intuitional epiphany has seen the more astute in the general field take the ball and run away with it. Fine for humanity perhaps, not so fine for its legacies.

So I'd like to take your offer of what could be quite valuable assistance under advisement for now. But please do prepare those further remarks in any case.

I use the phrase "selective environments" in the sense that evolutionary biologists use it, where the connotations are quite different than in ordinary language. If you don't understand how it's used in the field, you're ill-equipped to do an informed critique.

Selective environments make choices in precisely the same sense that rapidly moving water makes choices among bits of gravel of different sizes and weights, sorting the gravel bar below a rapids into a roughly ordered sequence according to size and weight.

RBH, you're simply wrong about choice, whatever the twist your favorite biologists put on the definition. My favorite evolutionary biologists see choice as a function of assessment and prediction, not as an assumption that all things predictAble were so by their own choices. Water does not choose, by the way, it obeys. The use of the word choice in the field is one form of the metaphor, the use in theoretical biology takes quite another form.And it's rare that the dogmatic such as yourself can objectively critique their own dogma.

My favorite evolutionary biologists see choice as a function of assessment and prediction, not as an assumption that all things predictAble were so by their own choices.

Then I'm sure you can name several of them, and can cite the references (publication and page) where the 'assessment and prediction' sense is used with reference to "selective environment and/or "natural selection."

RBH, I believe I have already done so. And I offered my latest comment in rebuttal to yours, which was a rebuttal of mine etc.. I see no need to complete a second or third circle of such. If my logical inference as to the role of choice in the web of causation is not to your deductive liking, so be it.

But RBH, wait, here are a couple of papers with what you may regard as a sort of tangential take on the subject (never afore cited here):Myths and Legends of the Baldwin Effecthttp://cogprints.org/2889/1/NRC-39220.pdf

Evolution, Learning, and Instinct: 100 Years of the Baldwin Effecthttp://www.geocities.com/Athens/4155/edit.html

And RBH, here's an article by a rather distinguished Philosophy of Science Professor, who may however by your standards also be ill-equiped to critique the field in question:http://www.kcl.ac.uk/ip/davidpapineau/Staff/Papineau/OnlinePapers/SocLearnBald.htm

Let me comment on e-man's citations one by one, in reverse order. The last is a "News and Commentary" piece in Nature describing a paper in a different journal that showed that some repetitive non-coding DNA, specifically Alu repeats, were apparently recruited as (parts of) functional exons in the Homo lineage, and are conserved and therefore apparently confer some selective advantage. There's nothing there about "choice and predictions" made by the process by which they were recruited.

The other three papers are about the Baldwin Effect. The second to last is (a) by a philosopher, not an evolutionary biologist as requested, and (b) describes the Baldwin Effect, known for on the order of a century. Aside from his apparent ignorance of pleiotropy (at least implicitly he seems to harbor a 'one gene, one trait' view), he gives a decent account of the Baldwin Effect and in fact proposes scenarios in which it may well have played a role in evolution. He even proposes a testable hypothesis, though it's problematic in some respects. None of it, however, implicates the general planful, foresighted notion of evolution elephantman apparently espouses.

The third to last, the Turney, et al. paper, is by guys in AI/IT/CS, not evolutionary biologists. The paper is again about the Baldwin Effect and attempts to incorporate it into computer-based evolutionary models incorporating neural networks. (Incidentally, I worked in that area for 15 years and have taught it at the college level.) Once again there is no reference to foresight or planning in the evolutionary algorithms.

Finally, the first citation is also to a paper on the Baldwin effect by Peter Turney, who is one of the authors of the preceding citation, and once again there's no reference to elephantman's conjectures about how evolutionary strategies work in biology.

So, one evolutionary biologist (Sorek) who doesn't mention e-man's contention, three non-biologists who don't mention it, no evolutionary biologists, and no references to "choice as a function of assessment and prediction" in biological evolution. Sorry, e-man.

RBH, as I said earlier, I have already cited evolutionary biologists, the most prominent being Lynn Margulis.These latter references were described as tangential, if you can discover what that means. The relevance is to the inadequacies of natural selection dogma in general - which is what this whole thread was to be about. The last citation referred to an actual selection mechanism making choices - how did you miss it? Unless you wanted to?And if you'd make more of an attempt to understand at least the next to last one, you'd see that choice as a function of assessment and prediction is what the Baldwin effect is at bottom all about. Can you honestly claim you've never heard of any such biological choice making concept?By the way, have you ever heard of a logic trap? because if you make that claim, you'll have just stepped into one.

man, I really am trying to understand what you're attempting to say, but as I noted earlier, it's difficult to parse some of your assertions.

For example, your claim about the Baldwin effect involving "choices" (in the context of natural selection and phenotypic plasticity creaqting conditions that lead to biological adaptation) as though that word means what it does in ordinary language (making decisions based on foresight and plans) is incomprehensible. Natural selection, whether plain old NS or NS operating to generate a heritable biological basis for learned behavioral traits that persist through generations, makes "choices" in exactly the same sense that a sieve makes choices.

There's a load of connotational baggage associated with the words you choose to use, and that baggage is pure noise (or, often, obfuscation) in the context of a technical discussion of a scientific subject.

RBH, you're ducking the question with all that bobbing and weaving as to whether you've heard of the biological choice making concept - which you must know is the basis for the Baldwin Effect controversy.

You write: 'Natural selection, whether plain old NS or NS operating to generate a heritable biological basis for learned behavioral traits that persist through generations, makes "choices" in exactly the same sense that a sieve makes choices.'

Classic. A sieve makes choices. Is this a sieve with assessment capabilities or a sorting mechanism? Can you identify any such sieve's location in or out of a particular organism?

Papineau wrote "-socially learned behaviour functions as an environmental niche that selects for its own innateness." Papineau would say that's choice directed selection, but then what would a guy like that know who can't recognize a sieve when he sees it?

And your idea of a technical discussion of selective mechanisms is to propose a sieve? Give us a break.

Admit that you've heard about biological choice so you can at least tell us what's wrong with the concept. The tactic of denying there is such a concept isn't cutting it. But I see the dilemma. You have to refrain from even contesting the Baldwin Effect hypothesis, because to do so would require the concession that it's exactly all about biological choice.

But I see the dilemma. You have to refrain from even contesting the Baldwin Effect hypothesis, because to do so would require the concession that it's exactly all about biological choice.

That reflects a profound ignorance of what the Baldwin effect is. Let me try to explain it, using the words of your references. As it happens, I've known about and understood it since the late 1960s, having done my undergraduate and graduate work then.

First, the notion of "phenotypic plasticity," defined in the "100 years" paper you provided:

In the context of this debate, James Mark Baldwin (1896) proposed "a new factor in evolution", whereby acquired characteristics could be indirectly inherited. Morgan (1896) and Osborn (1896) independently proposed similar ideas. The "new factor" was phenotypic plasticity: the ability of an organism to adapt to its environment during its lifetime. The ability to learn is the most obvious example of phenotypic plasticity, but other examples are the ability to tan with exposure to sun, to form a callus with exposure to abrasion, or to increase muscle strength with exercise.

No mention of "choice," no necessary assumption of "choosing." Just a population of organisms that display phenotypic plasticity (different from heritable variability). Note that none of the examples, including learning, implicate any choice at all.

Then continuing from the same paper:

The Baldwin effect works in two steps. First, phenotypic plasticity allows an individual to adapt to a partially successful mutation, which might otherwise be useless to the individual. If this mutation increases inclusive fitness, it will tend to proliferate in the population. However, phenotypic plasticity is typically costly for an individual. For example, learning requires energy and time, and it sometimes involves dangerous mistakes. Therefore there is a second step: given sufficient time, evolution may find a rigid mechanism that can replace the plastic mechanism. Thus a behavior that was once learned (the first step) may eventually become instinctive (the second step)

If the phenotypic variant has some selective -- reproductive -- advantage, and if mutations that support it occur and are therefore selected via differential reproductive success, then the trait or behavior may become based in the biology -- the genes -- rather than depending on social learning or adventitious phenotypic plasticity. The initially non-genetic variant becomes a genetically-based variant.

There's no "choice" there in any sense that carries the connotational baggage of planning, foresight, strategies anticipating the future, or any similar notion. If I have missed it in your references, please provide specific quotations -- where in those papers do we read about "biological choice," and specifically -- operationally -- what does "biological choice" mean in the context of the description of the Baldwin effect in your own reference.

RBH writes: 'There's no "choice" there in any sense that carries the connotational baggage of planning, foresight, strategies anticipating the future, or any similar notion.' Of course not. I've already written here that these are choice directed biological strategies - short term goal seeking through an incremental trial and error process. with no conception needed of the longer term ultimacy of such a process.

Here's a part of what it means operationally, found in the very paper we are now both referencing, Evolution, Learning, and Instinct: 100 Years of the Baldwin Effect, which you clearly didn't read, except to look for quotes you could take out of context.

"In biological organisms, learning can be driven by pleasure and pain. Turing (1950) argued that artificial intelligence researchers would be wise to build a pain-pleasure mechanism into their software. Most research in reinforcement learning examines how to learn from a reinforcement signal, but does not consider the origin of the signal. Batali and Grundy (this issue) call the pain-pleasure mechanism the "motivation system" and they investigate how motivation systems might evolve. Batali and Grundy show that interaction between a learning system and a motivation system can be much more complex and interesting than one might assume. The motivation system can evolve to encode regularities in the individual's evolutionary environment, which can simplify the learning task. On reflection, we can see that the motivation systems of biological organisms have a kind of "wisdom", which we tend to overlook."

Hardly consistent with your extrapolation from the carefully selected passages. Nor is it consistent with the re-eaximanation of the process done by Papineau, reflecting this has been an evolving concept since you first came across it.

I should add that my work is not about some adjunct to the Baldwin Effect. It's about biological strategies and the effects and ramifications of/from their heritability.The Baldwin Effect illustrates, at least theoretically, how the mechanism for such heritability can operate.Where the writings on the subject make reference to the strategies themselves, they tend to get it very wrong,IMHO.

Elephantman,I have looked briefly at your little barney with RBH, and I am getting puzzled about what you are writing an article about and whether it is a professional work or not. I have no idea about the article, but some of your statements in this forum are confusing to say the least. First you speak of evolutionary strategies as if you not only are familiar with the concept, but also as if you regard them as fundamental and in the normal evolutionary sense as metaphorical (no chess-master thinking things out, just any particular functional adaptation to a given niche or evolutionarily adaptive opportunity). Now you and RBH are in a shouting match that looks as if you regard selection in evolution as "real, literal selection", "conscious choice", or something like that. You will have a helluva selling job with that, and rightly, imo. If I understood your intention there correctly, it makes no sense to me that you could accept evolutionary strategies, but not accept "evolutionary choices" as being necessarily anything but what happens in an evolutionary strategy. Strategy is about choice. Your choices comprise your strategy if any, whether in a literal strategy or an evolutionary strategy. In the evolutionary strategy, your evolutionary choices are just an elementary application of the fundamental ideas of information. Do you have a more fundamental definition of information than: "material (aspects of) states that distinguish alternative possibilities"? In that light evolutionary strategies are direct analogies to conscious strategies, and evolutionary choices to conscious choices, and both are similarly subject to all the thermodynamic or formal aspects of information theory. But it leaves you mercilessly lumbered with that sieve you were girding at. What do you have against sieves? They seem simple enough to me. So far I see nothing in what you have said (Including in Baldwin effects) to support anything like "choice directed strategies ... biological - goal seeking ", whether in some sense conscious or not. And: "Water does not choose, by the way, it obeys. The use of the word choice in the field is one form of the metaphor, the use in theoretical biology takes quite another form." Those nasty biologists been fooling me long time, no? What is the difference between choice and "obedience" in such senses? One thing I can guarantee is that your elucidation of that metaphor had better be pretty cogent! And why for the love of mike do you have problems with selective environments? "They have a devil of a time with choices and predictions..." Zees ees a choke ja? What on earth are you thinking? If after this you remain interested, I'll try to get onto your multiple resistance problem, which strikes me as much of a non-problem.

Jon, that was good - now I can predict a bit more as to potential objections to my thesis from a slightly more philosophical stance than RBH and clones can muster up.First off, strategies aren't metaphorical, but the terms we must use to describe them will necessarily be metaphorical in the sense that we are limited to anthropocentric terminology for the most part when describing them. No they are not just any particular functional adaptation, etc. They are the means by which all organisms have "learned" to take advantage of "opportunity" (your metaphor, as cellular algorithms are not opportunistic as much as they are expectant or anticipatory). And of course you won't know what I'm talking about until I specify what some of them are, which I'm just not going to do here.Was I rough on RBH? Not really, but I needed to get him to speak up as a representative of the old school ideation. Of which you may well be another, and that's all to my good.Of course selection in evolution is not conscious choice. But yes, it IS dependent on a choice making process, which is what strategic systems are all about - they ASSESS situations and CHOOSE options.

But the way you and RBH seem to be using the term "evolutionary strategy" infers that the process itself has a strategy. It doesn't. It has resulted from differing individual strategies that have a common core. They don't however have a common goal overall. And spare me your little homily about elementary application of the fundamental ideas of information, a rationalization paradigm to obscure the fact that concepts like the archetypical sieve have none but the simplest powers of discernment.

If I haven't supported choice directed strategies to your satisfaction, it may because I shouldn't have to. You object to "goal seeking" while at the same time lecturing that strategies ARE about choice?Think perhaps about goal as a metaphor for something you will be happy to find by accident. That's the essence of trial and error efficacy, no?And choice is the essence of trial and error functionality, n'est-ce pas? (Man, I think I'm on a roll here.)

And really, do you think water is out on a trial and error search for a goal? Not unless it's the agent for some teleological chooser, I'd reckon. What is the difference between choice and obey, you ponder? Well one difference being that the term is usually not a reference to obeying your own choices, which water likely cannot do.And as to selective environment, just another "labeling" mechanism at work, pretending it covers a function in ways that will brook no further explanation. They make their own obedient choices and that's all the final causer wants us to know - right?Wrong. The environment activates the biological mechanism, which in turn will select its options, one of which s always to attempt to alter that very environment. Selections can be prompted by environment, not made. Unless you like fuzzy logic, always helpful a pinch, not as helpful fortesting out a theory.

As to my multiple resistance problem, I confess I didn't know I had one, but then I do accept that nobody's perfect.

Also I didn't think this was available for download, but here's the site:Modeling the Evolution of Motivation (1996) by John Batali , William Noble GrundyEvolutionary Computation

http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.37.5106

The authors state: "We refer to the mechanism by which an animal evaluates the fitness consequences of its actions as a "motivation system," and arguethat such a system must evolve along with the behaviors it evaluates."

Lots of other good stuff to cite, but I'll wait to see if anybody's here to read it. I suspect Jon and RBH have gone off together to try to arrange a variety of sieves in a series that will function as a prototypical algorithm. Also poking about in random fashion to find a niche to fit it to.

e-man, I really have tried to understand what you're arguing. I've read your references, and have thought about it. And I simply don't understand what you're trying to say. And I don't think it's my problem. Your way of expressing yourself in writing is opaquely allusive, you use words in non-standard ways, and it's very hard to figure out what you're trying to say. I suggest you work on your expository style if you hope to have any influence among informed readers.

RBH, the format of such a blog requires an idea to be condensed as a matter of space and reader interest.I hate long posts and suspect others find them suspect as well - length is not commensurate with persuasiveness in my view. But persuasion is seldom achieved in these forums where the emphasis is more likely to be on preaching to the crowd. You are not necessarily of the crowd that will be receptive to my version of heresy in any case. You have missed a lot of the meaning in the references accordingly. Go to Google Books and read the suggested book chapter on choice making functions - it's right there on line.Also my style is admittedly to test for reactions among the faithful. So I got a lot more out of the exchange than you did. Also if I revealed my core thesis it would have added to the clarity of the peripheral issues raised. But no could safely do.My work in progress is meant for public consumption in any case, not for an academic journal, or for the running of the per reviewers' gauntlet. They hate heresy even more than science blog aficionados, or than professional skeptics.Anyway thanks for your help, but I think I'm done here.

Hi elephantman >Jon, that was good - now I can predict a bit more as to potential objections to my thesis from a slightly more philosophical stance than RBH and clones can muster up.<I don't know why you are so shrill with RBH, and some others. The points he raises are reasonable, and if your thesis is to be worthy of discussion, that will be on the merits of its theme and logic, not the stridency of the author. Since I wrote the above (I actually am busy and have neglected commitments to gratify your wheedlings) I see you have added a few Parthian shots with Parthian courtesy to match. Do you have the faintest idea of the standard of ethics, never mind civility, corresponding to: "I suspect Jon and RBH have gone off together to try to arrange a variety of sieves in a series that will function as a prototypical algorithm. Also poking about in random fashion to find a niche to fit it to"? Do you imagine that guttersniping at professional competents whom you have importuned to help you in your incoherence of terminology and thought, is any substitute for either cogency or coherency? Gratuitous ascription of conspiracy against the integrity of your "thesis" is contemptible enough, without revealing your inability to tell from what we said that RBH and I had not the slightest need of recourse to each other for support in anything as trivial as this. You say: "My work in progress is meant for public consumption in any case, not for an academic journal, or for the running of the per reviewers' gauntlet. They hate heresy even more than science blog aficionados, or than professional skeptics." The perennial whine of the Forteans; their substitute for dignity. Heresy is for doctrine, not science. What you are describing is noise. Scepticism is something you had better steer clear of; you patently are incapable of understanding it; it is strong meat for tyros. RBH and I have independently tried to get you to say something, anything, substantial, and in a week or so, not a nibble! The best you can do is... "Also if I revealed my core thesis it would have added to the clarity of the peripheral issues raised. But no could safely do." Trust me on one thing, eman: you could hardly have been safer. Patently you still haven't learnt to distinguish between coffee tables and elephants. "I got a lot more out of the exchange than you did" -- yes, you got that right. What you did not get was any glimpse of insight into your own logical and technical bankruptcy. Bad luck! In case you do happen to look in again, then here is a closing request: Do let us know when your "thesis" for the public dawns on an astounded establishment. Since you never gave any intimation of any substance, I find myself curious to know just what you think it takes to aspire even to the cheap dignity of "heresy". Good luck,Jon

I leave all and sundry here with this quote from Biochemist Gerald Hazelbaue of the University of Missouri in Columbia, who says that, “Experience shows that if one can think of a possible mechanism for a particular biological process, no matter how strange or unusual, there is probably a biological system or organism that utilizes that mechanism.”

I see Jon, having given me a dose of his ridicule, couldn't take a bit of the jocular in return (didn't bother RBH all that much, but Jon may be a bit less secure with his self-image). Conspiracy to develop a prototypical algorithm? To use against my thesis?Hey, rest easy, Jon, it wouldn't have been about your paranoia, And yes, you got me - there wasn't any thesis - just having a little fun with the faux scientists here. Takes one to know one, right?

You should have explained it to the lesser intellects, the slow of perception. The ones who responded to your pleas for support.

Well, now is your chance to make good the lacunae in our perception. When you have finished laughing at it yourself, explain your witticism carefully and in great detail. I then will pass it round the Stalag so the rest if us will know when to laugh too when dealing with your sense of errr... wossname in future.

"Sweetheart, in all your girlish charm you are,Like laughter in a West End cinema.When lightning wisecracks flash and spurt and throng,Too loud my love, too late, and far too long." D.B.W.L.

Jon Richfield, My alleged pleas for support were the voices in your head that prompted your pleas to be let in on the secret. Which simply is that the higher levels of abstraction are an incomprehensible surreality to those of you forever stuck on the next lower. We call it reversing the sieve thermodynamically so that it becomes our floor and your roof. We can reach down to where you can't reach up from.

Jon Richfield hasn't had much luck with his own papers, but I hear the next one will reference the selection mechanism first discovered in Persia and will be a doozy - it's working title is Ali Baba and the Forty Sieves.

Has Jon Fairchild actually read Darwin's Dangerous Idea as he has claimed? Dennett wrote, "what Darwin discovered was not really one algorithm but, rather, a large class of related algorithms that he had no clear way to distinguish. We can now reformulate his fundamental idea as follows: Life on Earth has been generated over billions of tears in a single branching tree-the Tree of Life-by one algorithmic process or another."I'd say the E-man snookered Jon by substituting strategy for algorithm and Jon didn't catch the connection.

The above is not quite accurate The algorithms cited by Dennett served a purpose in nature but were not purposeful from the particular organism's point of view - in the sense that the strategies I'm concerned with serve the purposes of the organisms themselves.